In August 2020, the Office of the United Nations High Commissioner for Human Rights appointed Khan to the position of Special Rapporteur on freedom of expression and opinion.

[11] On January 23, 2024, Khan met with National Privacy Commission to examine the state of rights to freedom of opinion and expression in the Philippines.

[9] In her first year of office, she reformed Amnesty's response to human rights crises and launched the campaign to close the United States' Guantanamo Bay detention camp, which held suspected enemy combatants.

[9][14] During her leadership of IDLO, Irene Khan has promoted the notion that the rule of law is an important tool that can advance equity and people-centered development, whether in reducing inequalities or fostering social justice and inclusion for peace.

The film, shot in Colombia, Israel, Palestine and Pakistan, analyses how armed conflicts affect civilian communities and foster forced migration.

[24] In 2005, Irene Khan penned the introduction to that year's Amnesty International report in which she, inter alia, referred to the detention facility at Guantanamo Bay as "the gulag of our time," accusing the United States of "thumb[ing] its nose at the rule of law and human rights [as] it grants a licence to others to commit abuse with impunity".

[26] An editorial opinion in the Washington Post referred to it as "[i]t is ALWAYS SAD when a solid, trustworthy institution loses its bearings and joins in the partisan fracas that nowadays passes for political discourse".

"[28] In his The United Nations, Peace and Security, Ramesh Thakur called Khan's likening of the Guantanamo Bay detention facility to a gulag a "hyperbole" that is "wrong".

[38][39] Peter Pack, the chairman of Amnesty's International Executive Committee (IEC), initially stated on 19 February 2011: "The payments to outgoing secretary general Irene Khan shown in the accounts of AI (Amnesty International) Ltd for the year ending 31 March 2010 include payments made as part of a confidential agreement between AI Ltd and Irene Khan"[39] and that "It is a term of this agreement that no further comment on it will be made by either party.

Philip Davies, the Conservative MP for Shipley, decried the payment, telling the Daily Express: "I am sure people making donations to Amnesty, in the belief they are alleviating poverty, never dreamed they were subsidising a fat cat payout.

[38] He stated that "the new secretary general, with the full support of the IEC, has initiated a process to review our employment policies and procedures to ensure that such a situation does not happen again.

In the following months, IEC discovered that due to British employment law, it had to choose between the three options of either offering Khan a third term, discontinuing her post and, in their judgement, risking legal consequences, or signing a confidential agreement and issuing a pay compensation.

[40] Khan's lawyers issued a letter published by the Charity Times "It was not accurate of Amnesty International to record in its 2009/2010 corporate accounts that the amount £532,000 was paid to our client".

[41] The published letter detailed the sum as including: a) her salary and contractual benefits until 31 December 2009; b) outstanding back pay and the shortfall arising in her contractual benefits from previous years (in some part going back to 2005); relocation costs for her return abroad from where she had been recruited; d) compensation as well as severance payment (£115,000 gross) in respect of a legal claim and grievances that our client had asserted against Amnesty International Limited pursuant to her UK employment rights).